Base Info

An object of class Seurat 41753 features across 5594 samples within 2 assays Active assay: SCT (14486 features, 3000 variable features) 1 other assay present: RNA 3 dimensional reductions calculated: pca, umap, tsne

The Seurat object was generated with Seurat 3.1.4.

Table of Data

Tissue Data

Annotated Cell Types

Calculated Clusters

Interactive Plot

Downsampled to 5000 cells.

Environment

## R version 3.6.3 (2020-02-29)
## Platform: x86_64-apple-darwin18.7.0 (64-bit)
## Running under: macOS Mojave 10.14.6
## 
## Matrix products: default
## BLAS/LAPACK: /usr/local/Cellar/openblas/0.3.9/lib/libopenblasp-r0.3.9.dylib
## 
## locale:
## [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] Seurat_3.1.5   plotly_4.9.2.1 rmarkdown_2.1  knitr_1.28     dplyr_0.8.5   
## [6] ggplot2_3.3.0 
## 
## loaded via a namespace (and not attached):
##  [1] nlme_3.1-147        tsne_0.1-3          bitops_1.0-6       
##  [4] RcppAnnoy_0.0.16    RColorBrewer_1.1-2  httr_1.4.1         
##  [7] sctransform_0.2.1   tools_3.6.3         R6_2.4.1           
## [10] irlba_2.3.3         KernSmooth_2.23-16  uwot_0.1.8         
## [13] lazyeval_0.2.2      colorspace_1.4-1    npsurv_0.4-0       
## [16] withr_2.2.0         tidyselect_1.0.0    gridExtra_2.3      
## [19] compiler_3.6.3      labeling_0.3        caTools_1.18.0     
## [22] scales_1.1.0        lmtest_0.9-37       ggridges_0.5.2     
## [25] pbapply_1.4-2       stringr_1.4.0       digest_0.6.25      
## [28] pkgconfig_2.0.3     htmltools_0.4.0     htmlwidgets_1.5.1  
## [31] rlang_0.4.5         farver_2.0.3        zoo_1.8-7          
## [34] jsonlite_1.6.1      crosstalk_1.1.0.1   ica_1.0-2          
## [37] gtools_3.8.2        magrittr_1.5        patchwork_1.0.0    
## [40] Matrix_1.2-18       Rcpp_1.0.4.6        munsell_0.5.0      
## [43] ape_5.3             reticulate_1.15     lifecycle_0.2.0    
## [46] stringi_1.4.6       yaml_2.2.1          MASS_7.3-51.5      
## [49] gplots_3.0.3        Rtsne_0.15          plyr_1.8.6         
## [52] grid_3.6.3          parallel_3.6.3      gdata_2.18.0       
## [55] listenv_0.8.0       ggrepel_0.8.2       crayon_1.3.4       
## [58] lattice_0.20-41     cowplot_1.0.0       splines_3.6.3      
## [61] pillar_1.4.3        igraph_1.2.5        future.apply_1.5.0 
## [64] reshape2_1.4.4      codetools_0.2-16    leiden_0.3.3       
## [67] glue_1.4.0          evaluate_0.14       lsei_1.2-0         
## [70] data.table_1.12.8   vctrs_0.2.4         png_0.1-7          
## [73] gtable_0.3.0        RANN_2.6.1          purrr_0.3.4        
## [76] tidyr_1.0.2         future_1.17.0       assertthat_0.2.1   
## [79] xfun_0.13           rsvd_1.0.3          survival_3.1-12    
## [82] viridisLite_0.3.0   tibble_3.0.1        cluster_2.1.0      
## [85] globals_0.12.5      fitdistrplus_1.0-14 ellipsis_0.3.0     
## [88] ROCR_1.0-7